ArticleNucleic acids research2016
Crystal structure of a poly(rA) staggered zipper at acidic pH: evidence that adenine N1 protonation mediates parallel double helix formation.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Uracil-Peptide-Pyrene Conjugates as CuChembiochem : a European journal of chemical biology · 2026Article
- Single-Molecular Dissection of Liquid-Liquid Phase Transitions.Journal of the American Chemical Society · 2023Article
- Amyloid-like Hfq interaction with single-stranded DNA: involvement in recombination and replication inQRB discovery · 2022Article
- Parallel poly(A) homo- and hetero-duplex formation detection with an adapted DNA nanoswitch technique.RNA (New York, N.Y.) · 2020Article
- Anomalous Reverse Transcription through Chemical Modifications in Polyadenosine Stretches.Biochemistry · 2020Article
- The effect of adenine protonation on RNA phosphodiester backbone bond cleavage elucidated by deaza-nucleobase modifications and mass spectrometry.Nucleic acids research · 2019Article
- Adenine protonation enables cyclic-di-GMP binding to cyclic-GAMP sensing riboswitches.RNA (New York, N.Y.) · 2018Article
- Article
- A novel form of RNA double helix based on G·U and C·ARNA (New York, N.Y.) · 2018Article
- Influence of nucleotide modifications at the C2' position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA.Nucleic acids research · 2017Article
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4 authors.
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Abstract
We have solved at 1. 07: Å resolution the X-ray crystal structure of a polyriboadenylic acid (poly(rA)) parallel and continuous double helix. Fifty-nine years ago, double helices of poly(rA) were first proposed to form at acidic pH. Here, we show that 7-mer oligo(rA), i.e. rA7, hybridizes and overlaps in all registers at pH 3.5 to form stacked double helices that span the crystal. Under these conditions, rA7 forms well-ordered crystals, whereas rA6 forms fragile crystalline-like structures, and rA5, rA8 and rA11 fail to crystallize. Our findings support studies from ∼50 years ago: one showed using spectroscopic methods that duplex formation at pH 4.5 largely starts with rA7 and begins to plateau with rA8; another proposed a so-called 'staggered zipper' model in which oligo(rA) strands overlap in multiple registers to extend the helical duplex. While never shown, protonation of adenines at position N1 has been hypothesized to be critical for helix formation. Bond angles in our structure suggest that N1 is protonated on the adenines of every other rAMP-rAMP helix base pair. Our data offer new insights into poly(rA) duplex formation that may be useful in developing a pH sensor.
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